Chapter 1: Introduction . . 1
What is a microbe? . . 1
Why study microbial ecology? . . 1
How do we study microbes in nature? . . 10
The three kingdoms of life: Bacteria, Archaea, and Eukarya . . 12
Functional groups of microbes . . 15
Sources of background information . . 16

Chapter 2: Elements, biochemical;, and structures of microbes . . 19
Elemental composition of microbes . . 19
Elemental ratios in biogeochemical studies . . 21
C.N and C:P ratios for various microbes . . 22
Biochemical composition of bacteria . . 23
Explaining elemental ratios . . 25
Architecture of a microbial cell . . 26
Components of microbial cells as biomarkers . . 29
Extracellular structures . . 31

Chapter 3: Physical-chemical environment of microbes . . 35
Water . . 35
Temperature . . 36
pH . . 39
Salt and osmotic balance . . 40
Oxygen and redox potential . . 41
Light . . 42
Pressure . . 43
The consequences of being small . . 44
Microbial life in natural aquatic habitats . . 46
Microbial life in soils . . 49
The biofilm environment . . 51

Chapter 4: Microbial primary production and phototrophy . . 55
Basics of primary production and photosynthesis . . 55
Primary production, gross production, and net production . . 61
Primary production by terrestrial higher plants and aquatic microbes . . 63
The spring bloom and controls of phytoplankton growth . . 64
Major groups of bloom-forming phytoplankton . . 66
After the bloom: picoplankton and nanoplankton . .71
Primary production by coccoid cyanobacteria . . 73
Photoheterotrophy in the oceans . . 74

Chapter 5: Degradation of organic material . . 79
Mineralization of organic material in various ecosystems . . 80
Who does most of the respiration on the planet? . . 81
Chemical characterization of detrital organic material . . 84
Detrital food webs . . 86
DOM and the microbial loop . . 88
Hydrolysis of high molecular weight organic compounds . . 91
Uptake of low molecular weight organic compounds: turnover versus reservoir size . . 93
Chemical composition and organic material degradation . . 94
Release of inorganic nutrients and its control . . 96
Photo-oxidation of organic material . . 96
Refractory organic matter . . 97

Chapter 6: Microbial growth, biomass production, and controls . . 99
Are bacteria alive or dead? . . 99
Microbial growth and biomass production . . 102
Measuring growth and biomass production in nature . . 104
Bacterial biomass production in aquatic environments . . 105
Growth rates of bacteria and fungi in soils . . 108
What sets biomass production and growth by microbes in nature? . . 109
Competition and chemical communication between organisms . . 115

Chapter 7: Predation and protists . . 117
Bacterivory and herbivory in aquatic habitats . . 118
Grazers of bacteria and fungi in soils and sediments . . 120
Grazing mechanism for protists . . 121
Factors affecting grazing . . 122
Defenses against grazing . . 128
Effect of grazing on prey growth . . 129
Grazing by ciliates and dinoflagellates . . 129
Fluxes from microbial food webs to higher trophic levels . . 132
Mixotrophic protists and endosymbiosis . . 133

Chapter 8: Ecology of viruses . . 137
What are viruses? . . 137
Viral replication . . 138
Temperate viruses in nature . . 139
Contact between host and virus at the molecular scale . . 140
The number of viruses in natural environments . . 141
Mortality of bacteria due to viruses . . 146
Contribution of viruses versus grazers to bacterial mortality . . 147
Viral production and turnover . . 148
Viral decay and loss . . 148
Viruses of phytoplankton . . 149
Viruses are not grazers . . 150
Genetic exchange mediated by viruses . . 152

Chapter 9: Community structure of microbes in natural environments . . 157 
Taxonomy and phylogeny via genes . . 157
The species problem . . 159
Diversity of bacterial communities . . 160
The paradox of the plankton . . 162
Differences between cultivated and uncultivated microbes . . 163
Types of bacteria in soils, freshwaters, and the oceans . . 164
Archaea in non-extreme environment . . 166
Everything, everywhere? . . 167
What controls diversity levels and bacterial community structure? . . 168
Problems with 165 rRNA as a taxonomic and phyiogenetic tool . . 171
Community structure of protists and other eukaryotic microbes . . 173
Relevance of community structure to understanding processes . . 175

Chapter 10: Genomes and metagenomes of microbes and viruses . . 177
What are genomics and environmental genomics? . . 177
Turning genomic sequences into genomic information . . 178
Lessons from cultivated microbes . . 179
Genomes from uncultivated microbes: metagenomics . . 185
Metagenomics of a simple community in acid mine drainage . . 188
Useful compounds from metagenomics and activity screening . . 188
Metatranscriptomics and metaproteomics . . 189
Metagenomics of viruses .. 191

Chapter 11: Processes in anoxic environments . . 195
Introduction to anaerobic respiration . . 195
The order of electron acceptors . . 197
Oxidation of organic carbon by various electron acceptors . . 199
The anaerobic food chain . . 201
Sulfate reduction . . 204
Sulfur oxidation and the rest of the sulfur cycle . . 207
Methane and methanogenesis . . 210
Methanotrophy . . 212
Anaerobic eukaryotes . . 214

Chapter 12: The nitrogen cycle . . 217
Nitrogen fixation . . 218
Ammonium assimilation, regeneration, and fluxes . . 221
Ammonia oxidation, nitrate production, and nitrification . . 224
Nitrite oxidation and the second step in nitrification . . 229
Anaerobic ammonia oxidation . . 229
Dissimilatory nitrate reduction and denitrification . . 230
Denitrification versus anaerobic ammonium oxidation . . 232'
Sources and sinks of nitrous oxide . . 233
Balancing N loss and N2 fixation . . 234

Chapter 13: Introduction to geomicrobiology . . 237
Cell surface charge, metal sorption, and microbial attachment . . 237
Attachment of microbes to surfaces . . 241
Biomineralization by microbes . . 241
Manganese and iron-oxidizing bacteria . . 248
Weathering and mineral dissolution by microbes . . 251
Geomicrobiology of fossil fuels . . 253

Chapter 14: Symbiosis and microbes . . 257
Microbial residents of vertebrates . . 259
Microbial symbioses with insects . . 261
Symbiotic microbes in marine invertebrates . . 265
Microbe-plant symbioses . . 271
Concluding remarks . . 275

References . . 277
Index . . 303